My Smart mailboxes are messed up in Mavericks

Does anyone have a fix for my messed up smart mailboxes?
The counts are wrong and the filtering I set up doesn't seem to work.
For example, I have an 'unread' smart mailbox which shows 1 unread message but has a count of 7.
I have another mailbox called 'recent' set to exclude shopping and forum related email: it's all in there and the count is wrong too.
(Sorry if there's any bad spelling - Safari doesn't pay attention to my 'Check Spelling' setting any more under Mavericks)

Here's what I did to fix it (but I cannot confirm that it stays fixed): I redid my spotlight index. Mail uses spotlight to implement its smart mailboxes.
Here's how I did it:
open Terminal app
sudo mdutil -E /
mdutil is the unix command to manage the meta data store (which is what implements spotlight) and the -E argument means "erase and rebuild the index". Here's the output from my Terminal session (my laptop name is montepulciano):
$ sudo mdutil -sa
Password:
          Indexing enabled.
/.MobileBackups:
2013-10-26 22:45:23.563 mdutil[4242:507] Metadata.framework [Error]: mdsCopyStoreAttributes failed: (8) (os/kern) no access
          No index.
/Volumes/Main:
          Indexing enabled.
/Volumes/Main/Backups.backupdb:
          Indexing enabled.
[montepulciano:22:45:23::~]
$ sudo mdutil -E /
          Indexing enabled.
[montepulciano:22:45:49::~]
$
After I ran the last command my CPUs got very busy and it took about an hour to rebuild the index.

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